fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index fe80b7810e716264152835060f25d1f2e45c1fed..24142e0cf4aa6174a8006f1e0a7a85c82f10ab24 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -122,7 +122,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                        else if (mapfile == "not found") {  mapfile = "";  m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; }        
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not open") { abort = true; }
+                       if (fastafile == "not open") { fastafile = ""; abort = true; }
                        else if (fastafile == "not found") {                            
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
@@ -139,7 +139,11 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                outputDir = ""; 
                                outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
-
+                       
+                       if ((namefile == "") && (fastafile != "")){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
                }
 
        }